Bugs item #3561720, was opened at 2012-08-25 09:13
Message generated for change (Comment added) made by hansonr
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Category: Application
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: k. siegmund (iridos)
Assigned to: Bob Hanson (hansonr)
Summary: Please don't auto-detect of best representation on load
Initial Comment:
Hi,
when loading files from the gui interface, the types of molecules in the file
is auto-detected and the appropriate representation chosen.
This _only_ happens when a (pdb) file is loaded from the gui, not when a pdb
entry is fetched from the net or a file is specified via the commandline.
What's worse, autodetect sometimes fails (e.g. on single amino/nucleic acids
e.g. guanosine) and no molecule is shown.
Please make it an option in GUI to switch between default and autodetected
representation.
Cheers,
I.
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>Comment By: Bob Hanson (hansonr)
Date: 2012-08-29 05:26
Message:
Yes, thanks. That makes it clearer. "Autodetection" for me was in relation
to determining file type, not rendering. The cartoon-rendering script
reads:
zap; load "C:/jmol-dev/bobtest/1crn.pdb";if (_loadScript = '' &&
defaultLoadScript == '' && _filetype == 'Pdb') { select protein or
nucleic;cartoons Only;color structure; select * }
so all you have to do is
set defaultLoadScript " "
to turn that automated rendering off.
----------------------------------------------------------------------
Comment By: k. siegmund (iridos)
Date: 2012-08-29 01:19
Message:
Sorry for the delay...
When I open a file from the commandline, e.g.jmol 2BQ2.pdb.gz (which is
PDB entry 2BQ2), then I get a balls-and-sticks representation of the
molecule (a short piece of DNA) and "history" of the console shows "load
"2BQ2.pdb.gz"
Loading a structure via "file->get PDB" again results in a ball-and-stick
representation
If i use the GUI instead to open the same file (File->open), the console
shows:
zap; load "file:///[...]2BQ2.pdb.gz";if (_loadScript = '' &&
defaultLoadScript == '' && _filetype == 'Pdb') { select protein or
nucleic;cartoons Only;color structure; select * }
Consequently, all protein/DNA moieties are displayed in a cartoon
representation.
This is ok if it works, but pretty annoying if it doesnt... loading a file
with just one guanine molecule is detected as DNA, but a
cartoon-representation of a single molecule is an empty screen. While
that's a separate bug as such, I think the bigger problem is, that
auto-detection can fail in various ways and so the user should have control
to switch it on and off?
Hope that helped to make my first post clearer.
cheers,
I.
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2012-08-25 16:14
Message:
Also -- I don't see how there could be no difference between any of these
loads -- the exact same methods are executed. So very important to provide
the exact commands you are giving that seem to be causing the problem.
Version of Jmol?
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2012-08-25 15:12
Message:
Sorry, you will have to be more specific. What exactly are you trying to
do, what is the site in question, and where is the problem? It sounds to me
like the site you are using for the source of files is not serving up good
PDB files. I'd like to see some of them...
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3561720&group_id=23629
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